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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ), 'gf_id' => 'HOM05D001128', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001128' ), 'data_identifier' => 'HOM05D001128', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001128', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '546', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p05780' => 'bna', 'A07p21900' => 'bna', 'A09p46920' => 'bna', 'Aa31LG10G8860' => 'aar', 'Aa31LG5G19750' => 'aar', 'Actinidia02379' => 'ach', 'Actinidia02898' => 'ach', 'Actinidia12878' => 'ach', 'Actinidia13814' => 'ach', 'Actinidia13898' => 'ach', 'Actinidia13925' => 'ach', 'Actinidia14078' => 'ach', 'Actinidia21110' => 'ach', 'Actinidia28180' => 'ach', 'Actinidia29161' => 'ach', 'Ah.02g119490' => 'amhyb', 'Ah.03g148320' => 'amhyb', 'Ah.10g036830' => 'amhyb', 'AL5G35000' => 'aly', 'Aqoxy1G00786' => 'aox', 'Aqoxy2G03314' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1NAQ44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.463IUL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74AGPN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BMML80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E0Q1QR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EVQB8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBQI3L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2YSCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKI1B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3CEFB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U326PE' => 'arhy', 'AT3G54000' => 'ath', 'ATR0210G013' => 'atr', 'Atru.chr12.272' => 'acertr', 'Atru.chr3.4033' => 'acertr', 'Atru.chr5.1430' => 'acertr', 'Atru.chr8.2106' => 'acertr', 'AUR62003387' => 'cqu', 'AUR62012167' => 'cqu', 'AUR62022804' => 'cqu', 'AUR62029443' => 'cqu', 'BcaB01g00225' => 'bca', 'BcaB02g07755' => 'bca', 'BcaB02g07756' => 'bca', 'BcaB02g08495' => 'bca', 'BcaC02g09109' => 'bca', 'BcaC07g39751' => 'bca', 'BcaC08g44658' => 'bca', 'BolC4t25433H' => 'bol', 'BolC6t37368H' => 'bol', 'BolC8t50527H' => 'bol', 'BraA04t16274Z' => 'bra', 'BraA07t29871Z' => 'bra', 'BraA09t40159Z' => 'bra', 'C04p38580' => 'bna', 'C06p21800' => 'bna', 'C08p29250' => 'bna', 'CAN.G394.85' => 'can', 'CANSAT25G3618' => 'cansat', 'CANSAT35G1304' => 'cansat', 'CANSAT56G2245' => 'cansat', 'CANSAT56G3374' => 'cansat', 'CARHR163900' => 'chi', 'Carub.0005s2059' => 'cru', 'Ca_01300_v3' => 'car', 'Ca_05146_v3' => 'car', 'Ca_05916_v3' => 'car', 'Ca_07581_v3' => 'car', 'Ca_17132_v3' => 'car', 'Ca_20607_v3' => 'car', 'Ca_29561_v3' => 'car', 'CBR_g8011' => 'cbr', 'Cc01_g13540' => 'ccan', 'Cc02_g07190' => 'ccan', 'Cc06_g02010' => 'ccan', 'CDE02G1727' => 'cde', 'CDE02G2787' => 'cde', 'CDE03G0277' => 'cde', 'CDE04G0001' => 'cde', 'CDE04G3507' => 'cde', 'CDE09G1396' => 'cde', 'Cfa001394' => 'cfa', 'Cfa011590' => 'cfa', 'Cfa017294' => 'cfa', 'Ciclev10011799m.g' => 'ccl', 'Ciclev10023667m.g' => 'ccl', 'Ciclev10029021m.g' => 'ccl', 'Ciclev10031729m.g' => 'ccl', 'CiPaw.01G293700' => 'cil', 'CiPaw.02G188400' => 'cil', 'CiPaw.08G105000' => 'cil', 'CiPaw.09G202700' => 'cil', 'CiPaw.10G150200' => 'cil', 'CiPaw.13G086900' => 'cil', 'CiPaw.14G063600' => 'cil', 'ClCG00G003060' => 'cla', 'ClCG04G007510' => 'cla', 'ClCG07G003770' => 'cla', 'ClCG09G006980' => 'cla', 'ClCG10G021590' => 'cla', 'ClCG10G021600' => 'cla', 'ClCG11G006470' => 'cla', 'COL.COLO4_14683' => 'col', 'COL.COLO4_25581' => 'col', 'Cpa.g.sc19.247' => 'cpa', 'Cpa.g.sc52.31' => 'cpa', 'Cpa.g.sc56.66' => 'cpa', 'Cpa.g.sc81.51' => 'cpa', 'CsaV3_3G034420' => 'csa', 'CsaV3_3G034430' => 'csa', 'CsaV3_4G025740' => 'csa', 'CsaV3_5G008580' => 'csa', 'CsaV3_6G001520' => 'csa', 'CsaV3_7G028180' => 'csa', 'CSS0004370' => 'camsi', 'CSS0013156' => 'camsi', 'CSS0014150' => 'camsi', 'CSS0027233' => 'camsi', 'CSS0030928' => 'camsi', 'CSS0032417' => 'camsi', 'CSS0047983' => 'camsi', 'DCAR_005928' => 'dca', 'DCAR_007415' => 'dca', 'DCAR_010429' => 'dca', 'DCAR_012149' => 'dca', 'DCAR_018932' => 'dca', 'DCAR_024850' => 'dca', 'DCAR_028803' => 'dca', 'Dinv16282' => 'din', 'Dinv17068' => 'din', 'Dinv32942' => 'din', 'Dinv34306' => 'din', 'Dinv34448' => 'din', 'Dinv35538' => 'din', 'Dinv37107' => 'din', 'Dinv37108' => 'din', 'Dinv43012' => 'din', 'Dinv43085' => 'din', 'Duzib093G0147' => 'dzi', 'Duzib106G0325' => 'dzi', 'Duzib106G0526' => 'dzi', 'Duzib114G0703' => 'dzi', 'Duzib128G0075' => 'dzi', 'Duzib128G2050' => 'dzi', 'Duzib138G1095' => 'dzi', 'Duzib150G0620' => 'dzi', 'Duzib168G0052' => 'dzi', 'Duzib170G1159' => 'dzi', 'Duzib211G0347' => 'dzi', 'ECA236G1029' => 'eca', 'ECA236G1683' => 'eca', 'ECA238G0704' => 'eca', 'ECA247G0052' => 'eca', 'ECA248G1741' => 'eca', 'EL10Ac2g04665' => 'bvu', 'EL10Ac6g15458' => 'bvu', 'Eucgr.B02293' => 'egr', 'Eucgr.B02733' => 'egr', 'Eucgr.J00969' => 'egr', 'Eucgr.J01995' => 'egr', 'Eucgr.K03018' => 'egr', 'Eucgr.K03372' => 'egr', 'FAN01G1897' => 'fan', 'FAN02G4298' => 'fan', 'FAN03G2145' => 'fan', 'FAN05G2922' => 'fan', 'FAN06G2816' => 'fan', 'FAN06G3577' => 'fan', 'FAN09G1692' => 'fan', 'FAN10G3504' => 'fan', 'FAN11G2007' => 'fan', 'FAN14G3619' => 'fan', 'FAN15G2738' => 'fan', 'FAN16G1449' => 'fan', 'FAN20G0154' => 'fan', 'FAN21G1564' => 'fan', 'FAN24G2693' => 'fan', 'FAN25G3787' => 'fan', 'FAN27G0408' => 'fan', 'FvH4_2g23650' => 'fve', 'FvH4_3g37230' => 'fve', 'FvH4_6g12650' => 'fve', 'FvH4_7g23630' => 'fve', 'Glyma.01G106500' => 'gma', 'Glyma.02G147700' => 'gma', 'Glyma.02G252700' => 'gma', 'Glyma.03G073712' => 'gma', 'Glyma.03G153200' => 'gma', 'Glyma.07G141000' => 'gma', 'Glyma.10G026100' => 'gma', 'Glyma.11G134800' => 'gma', 'Glyma.11G225400' => 'gma', 'Glyma.12G058400' => 'gma', 'Glyma.13G339500' => 'gma', 'Glyma.14G063900' => 'gma', 'Glyma.15G034900' => 'gma', 'Glyma.18G031800' => 'gma', 'Glyma.18G191000' => 'gma', 'Glyma.19G155600' => 'gma', 'Gohir.A03G046700' => 'ghi', 'Gohir.A04G086100' => 'ghi', 'Gohir.A05G091900' => 'ghi', 'Gohir.A05G346700' => 'ghi', 'Gohir.A06G165300' => 'ghi', 'Gohir.A08G067900' => 'ghi', 'Gohir.A09G161600' => 'ghi', 'Gohir.A10G226400' => 'ghi', 'Gohir.A11G328200' => 'ghi', 'Gohir.D03G120500' => 'ghi', 'Gohir.D04G065500' => 'ghi', 'Gohir.D04G126000' => 'ghi', 'Gohir.D05G092700' => 'ghi', 'Gohir.D06G170700' => 'ghi', 'Gohir.D08G076400' => 'ghi', 'Gohir.D09G157200' => 'ghi', 'Gohir.D10G238700' => 'ghi', 'Gohir.D11G347100' => 'ghi', 'Gorai.003G127200' => 'gra', 'Gorai.004G080700' => 'gra', 'Gorai.006G178800' => 'gra', 'Gorai.007G377500' => 'gra', 'Gorai.009G095300' => 'gra', 'Gorai.010G199700' => 'gra', 'Gorai.011G274600' => 'gra', 'Gorai.012G073700' => 'gra', 'Gorai.012G109000' => 'gra', 'GSVIVG01002073001' => 'vvi', 'GSVIVG01007626001' => 'vvi', 'GSVIVG01011088001' => 'vvi', 'GSVIVG01012944001' => 'vvi', 'GSVIVG01016431001' => 'vvi', 'GSVIVG01024844001' => 'vvi', 'GSVIVG01026841001' => 'vvi', 'GSVIVG01034054001' => 'vvi', 'GSVIVG01038461001' => 'vvi', 'HanXRQChr01g0003181' => 'han', 'HanXRQChr04g0124601' => 'han', 'HanXRQChr05g0149921' => 'han', 'HanXRQChr06g0176291' => 'han', 'HanXRQChr07g0202001' => 'han', 'HanXRQChr08g0212731' => 'han', 'HanXRQChr08g0221301' => 'han', 'HanXRQChr10g0292031' => 'han', 'HanXRQChr12g0369451' => 'han', 'HanXRQChr14g0458491' => 'han', 'Haze_01692' => 'cav', 'Haze_04722' => 'cav', 'Haze_17155' => 'cav', 'Haze_20899' => 'cav', 'Haze_24208' => 'cav', 'Hma1.2p1_0026F.1_g016650' => 'hma', 'Hma1.2p1_0039F.1_g024950' => 'hma', 'Hma1.2p1_0671F.1_g200660' => 'hma', 'Hma1.2p1_1521F.1_g288670' => 'hma', 'HPP92_015345' => 'vpl', 'HPP92_018162' => 'vpl', 'HPP92_018175' => 'vpl', 'HPP92_026966' => 'vpl', 'Hund05343' => 'sun', 'Hund12841' => 'sun', 'Hund13813' => 'sun', 'Hund16030' => 'sun', 'Lalb_Chr03g0042761' => 'lal', 'Lalb_Chr04g0250911' => 'lal', 'Lalb_Chr06g0163041' => 'lal', 'Lalb_Chr10g0104881' => 'lal', 'Lalb_Chr13g0291891' => 'lal', 'Lalb_Chr14g0372071' => 'lal', 'Lalb_Chr15g0084451' => 'lal', 'Lalb_Chr17g0346461' => 'lal', 'Lalb_Chr18g0052901' => 'lal', 'Lalb_Chr19g0124971' => 'lal', 'Lalb_Chr19g0138041' => 'lal', 'Lalb_Chr24g0397131' => 'lal', 'Lj1A945T19' => 'lonja', 'Lj1A946G35' => 'lonja', 'Lj1g0006514' => 'lja', 'Lj1g0009897' => 'lja', 'Lj2A85T61' => 'lonja', 'Lj3C959G13' => 'lonja', 'Lj3g0022973' => 'lja', 'Lj6g0007644' => 'lja', 'LjContig00047_ERROPOS266959g0024685' => 'lja', 'LjContig00141g0001836' => 'lja', 'Lsat_1_v5_gn_2_116981' => 'lsa', 'Lsat_1_v5_gn_5_168381' => 'lsa', 'Lsat_1_v5_gn_5_188320' => 'lsa', 'Lsat_1_v5_gn_8_14501' => 'lsa', 'Lsat_1_v5_gn_8_72501' => 'lsa', 'Lsat_1_v5_gn_8_80861' => 'lsa', 'Lsat_1_v5_gn_9_16140' => 'lsa', 'Lsat_1_v5_gn_9_31700' => 'lsa', 'Manes.01G167300' => 'mes', 'Manes.01G208200' => 'mes', 'Manes.02G125700' => 'mes', 'Manes.05G075700' => 'mes', 'Manes.07G123000' => 'mes', 'Manes.07G123100' => 'mes', 'Manes.09G099100' => 'mes', 'Manes.10G020700' => 'mes', 'Manes.10G020800' => 'mes', 'Mapoly0094s0056' => 'mpo', 'MBI05_g02674_MAGBIO' => 'mbi', 'MBI14_g02856_MAGBIO' => 'mbi', 'MD01G1142200' => 'mdo', 'MD03G1082700' => 'mdo', 'MD03G1266000' => 'mdo', 'MD04G1140200' => 'mdo', 'MD07G1207900' => 'mdo', 'MD11G1090800' => 'mdo', 'MD11G1286400' => 'mdo', 'MD12G1155400' => 'mdo', 'MD15G1149300' => 'mdo', 'Medtr0027s0090' => 'mtr', 'Medtr1g072310' => 'mtr', 'Medtr2g097800' => 'mtr', 'Medtr3g069670' => 'mtr', 'Medtr4g019840' => 'mtr', 'Medtr4g064947' => 'mtr', 'Medtr5g081460' => 'mtr', 'MELO3C003199.2' => 'cme', 'MELO3C008261.2' => 'cme', 'MELO3C009212.2' => 'cme', 'MELO3C009213.2' => 'cme', 'MELO3C015842.2' => 'cme', 'MELO3C026566.2' => 'cme', 'Migut.D00291' => 'egut', 'Migut.F00730' => 'egut', 'Migut.F01305' => 'egut', 'Migut.J00260' => 'egut', 'Migut.L01977' => 'egut', 'Migut.N00909' => 'egut', 'MSTRG.10240' => 'ama', 'MSTRG.12657' => 'ama', 'MSTRG.17824' => 'ama', 'MSTRG.19049' => 'ama', 'MSTRG.21564' => 'ama', 'MSTRG.26788' => 'ama', 'MSTRG.27358' => 'ama', 'MSTRG.5621' => 'ama', 'MSTRG.8291' => 'ama', 'Nitab4.5_0000008g0230' => 'nta', 'Nitab4.5_0000119g0370' => 'nta', 'Nitab4.5_0000243g0040' => 'nta', 'Nitab4.5_0000652g0060' => 'nta', 'Nitab4.5_0000744g0010' => 'nta', 'Nitab4.5_0002822g0050' => 'nta', 'Nitab4.5_0002823g0030' => 'nta', 'Nitab4.5_0003264g0030' => 'nta', 'Nitab4.5_0009885g0020' => 'nta', 'Nitab4.5_0011623g0010' => 'nta', 'Nn1g00216' => 'nnu', 'Nn1g00331' => 'nnu', 'Nn1g02211' => 'nnu', 'Nn2g11296' => 'nnu', 'Nn2g13535' => 'nnu', 'Nn3g17868' => 'nnu', 'Nn3g19140' => 'nnu', 'Nn3g21621' => 'nnu', 'Nn4g26238' => 'nnu', 'Nn8g40397' => 'nnu', 'Oeu001830.1' => 'oeu', 'Oeu007672.1' => 'oeu', 'Oeu009915.1' => 'oeu', 'Oeu013161.1' => 'oeu', 'Oeu018335.1' => 'oeu', 'Oeu018987.1' => 'oeu', 'Oeu024612.2' => 'oeu', 'Oeu028076.1' => 'oeu', 'Oeu028077.1' => 'oeu', 'Oeu032139.1' => 'oeu', 'Oeu035129.1' => 'oeu', 'Oeu041717.1' => 'oeu', 'Os01g0850000' => 'osa', 'Os05g0453300' => 'osa', 'Peaxi162Scf00009g03319' => 'pax', 'Peaxi162Scf00014g01511' => 'pax', 'Peaxi162Scf00132g00911' => 'pax', 'Peaxi162Scf00481g00624' => 'pax', 'Peaxi162Scf01622g00014' => 'pax', 'PGR004G1424' => 'pgr', 'PGR031G3883' => 'pgr', 'PGR044G0160' => 'pgr', 'PGR044G1404' => 'pgr', 'PGR119G0644' => 'pgr', 'PGSC0003DMG400011013' => 'stu', 'PGSC0003DMG400011730' => 'stu', 'PGSC0003DMG400019191' => 'stu', 'PGSC0003DMG400030336' => 'stu', 'Phvul.001G150600' => 'pvu', 'Phvul.001G238700' => 'pvu', 'Phvul.007G171600' => 'pvu', 'Phvul.008G113400' => 'pvu', 'Phvul.008G228300' => 'pvu', 'Phvul.011G060600' => 'pvu', 'Phvul.L008643' => 'pvu', 'Potri.002G053700' => 'ptr', 'Potri.005G208800' => 'ptr', 'Potri.006G093000' => 'ptr', 'Potri.008G062200' => 'ptr', 'Potri.009G038600' => 'ptr', 'Potri.010G195800' => 'ptr', 'Potri.016G105000' => 'ptr', 'Prupe.2G243200' => 'ppe', 'Prupe.4G251600' => 'ppe', 'Prupe.6G067000' => 'ppe', 'Prupe.6G265300' => 'ppe', 'Prupe.8G241700' => 'ppe', 'Psat0s1845g0240' => 'psa', 'Psat2g036720' => 'psa', 'Psat5g125600' => 'psa', 'Psat5g286040' => 'psa', 'Psat6g060440' => 'psa', 'Psat7g211520' => 'psa', 'Psat7g240440' => 'psa', 'PSO339G4622' => 'pso', 'PSO384G2375' => 'pso', 'PSO541G6419' => 'pso', 'PSO675G1334' => 'pso', 'QL01p028290' => 'qlo', 'QL07p027947' => 'qlo', 'QL08p062120' => 'qlo', 'QL12p021827' => 'qlo', 'QL12p021963' => 'qlo', 'RcHm_v2.0_Chr1g0368901' => 'rch', 'RcHm_v2.0_Chr3g0464501' => 'rch', 'RcHm_v2.0_Chr5g0066981' => 'rch', 'RcHm_v2.0_Chr6g0291121' => 'rch', 'Rhsim03G0138400' => 'rsi', 'Rhsim05G0200600' => 'rsi', 'Rhsim13G0075900' => 'rsi', 'Sabra02G0043700' => 'sbr', 'Sabra05G0158900' => 'sbr', 'Sabra06G0070700' => 'sbr', 'Sabra08G0045800' => 'sbr', 'Sabra09G0027500' => 'sbr', 'Sabra10G0150300' => 'sbr', 'Sabra16G0104100' => 'sbr', 'SalBow1G2079' => 'sbo', 'SalBow2G1629' => 'sbo', 'SalBow4G0348' => 'sbo', 'SalBow4G1333' => 'sbo', 'SalBow5G3624' => 'sbo', 'SalBow6G4034' => 'sbo', 'SalBow6G5364' => 'sbo', 'SalBow6G5821' => 'sbo', 'Sc07g0006950' => 'sci', 'Sc10g0001950' => 'sci', 'Sc11g0007590' => 'sci', 'Sc14g0004740' => 'sci', 'Sc17g0004110' => 'sci', 'Sc22g0004330' => 'sci', 'Sed0002927' => 'sed', 'Sed0012315' => 'sed', 'Sed0015993' => 'sed', 'Sed0016602' => 'sed', 'Sed0016661' => 'sed', 'Sed0019989' => 'sed', 'Sed0021418' => 'sed', 'Sed0022303' => 'sed', 'Sed0023317' => 'sed', 'Sed0025256' => 'sed', 'SEGI_03969' => 'sgi', 'SEGI_15940' => 'sgi', 'SEGI_27945' => 'sgi', 'SGA_v2.0_scaffold104G30158' => 'sas', 'SGA_v2.0_scaffold199G41168' => 'sas', 'SGA_v2.0_scaffold1G00467' => 'sas', 'SGA_v2.0_scaffold453G51859' => 'sas', 'SGA_v2.0_scaffold85G26810' => 'sas', 'SGA_v2.0_scaffold94G28557' => 'sas', 'SHI03582' => 'shi', 'SMO171G0071' => 'smo', 'SMO353G0321' => 'smo', 'SMO367G0607' => 'smo', 'Solyc06g076490.3' => 'sly', 'Solyc09g011690.4' => 'sly', 'Solyc10g084970.2' => 'sly', 'Sopen06g032900' => 'spe', 'Sopen09g006510' => 'spe', 'Sopen10g034430' => 'spe', 'Sp5g08400' => 'spa', 'TAR369G0362' => 'tar', 'TAR369G0849' => 'tar', 'TAR623G0478' => 'tar', 'TAR633G0212' => 'tar', 'TAR633G0329' => 'tar', 'TAR636G2726' => 'tar', 'THA.LOC104805648' => 'tha', 'THA.LOC104806538' => 'tha', 'THA.LOC104809429' => 'tha', 'THA.LOC104810062' => 'tha', 'THA.LOC104823397' => 'tha', 'THA.LOC104824295' => 'tha', 'Thecc.01G280100' => 'tca', 'Thecc.05G027900' => 'tca', 'Thecc.09G311600' => 'tca', 'Thecc.10G030500' => 'tca', 'Thhalv10010478m.g' => 'esa', 'TPR.G11407' => 'tpr', 'TPR.G13630' => 'tpr', 'TPR.G17896' => 'tpr', 'TPR.G23629' => 'tpr', 'TPR.G25845' => 'tpr', 'TPR.G6832' => 'tpr', 'TPR.G7175' => 'tpr', 'TPR.G9121' => 'tpr', 'TWI09G0818' => 'twi', 'TWI14G0703' => 'twi', 'TWI53G0706' => 'twi', 'TWI59G0791' => 'twi', 'TWI74G1371' => 'twi', 'TWI75G1051' => 'twi', 'TWI77G0372' => 'twi', 'TWI79G1361' => 'twi', 'unitig_22.g6581' => 'ugi', 'unitig_26.g9107' => 'ugi', 'unitig_46.g18411' => 'ugi', 'unitig_578.g15885' => 'ugi', 'unitig_746.g26718' => 'ugi', 'unitig_748.g6991' => 'ugi', 'unitig_749.g14177' => 'ugi', 'unitig_8.g4426' => 'ugi', 'unitig_899.g15262' => 'ugi', 'vmacro03017' => 'vma', 'vmacro07011' => 'vma', 'vmacro20201' => 'vma', 'VMungo0251G1217' => 'vmu', 'VMungo0464G0262' => 'vmu', 'VMungo0464G0499' => 'vmu', 'VMungo0647G0267' => 'vmu', 'VMungo0720G0300' => 'vmu', 'VMungo0720G0374' => 'vmu', 'VMungo0720G0772' => 'vmu', 'VMungo1080G0292' => 'vmu', 'VMungo1127G1222' => 'vmu', 'VMungo1127G1603' => 'vmu', 'VMungo1215G3461' => 'vmu', 'VMungo1383G0733' => 'vmu', 'VMungo1383G1773' => 'vmu', 'VMungo1383G2279' => 'vmu', 'Zm00001eb147910' => 'zma', 'Zm00001eb289430' => 'zma', 'Zm00001eb347770' => 'zma', 'Zm00001eb367680' => 'zma' ) $gf_id = 'HOM05D001128' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001128' ) $data_identifier = 'HOM05D001128' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 7, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 7, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 6, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 11, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 16, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 9, 'han' => (int) 10, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 12, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 9, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 7, 'cme' => (int) 6, 'egut' => (int) 6, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 10, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppe' => (int) 5, 'psa' => (int) 7, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 10, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 8, 'twi' => (int) 8, 'ugi' => (int) 9, 'vma' => (int) 3, 'vmu' => (int) 14, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367680' $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